Simulation studies of stratum corneum lipid mixtures

Molecular dynamics simulations of lipid composition and its impact on structural and dynamic properties of skin membrane

The stratum corneum (SC) plays the most important role in the absorption of topical and transdermal drugs. In this study, we developed a multi-layered SC model using coarse-grained molecular dynamics (CGMD) simulations of ceramides, cholesterol, and fatty acids in equimolar proportions, starting from two different initial configurations. In the first approach, all ceramide molecules were initially in the hairpin conformation, and the membrane bilayers were pre-formed. In the second approach, ceramide molecules were introduced in either the hairpin or splayed conformation, with the lipid molecules randomly oriented at the start of the simulation. The aim was to evaluate the effects of lipid chain length on the structural and dynamic properties of SC. By incorporating ceramides and fatty acids of different chain lengths, we simulated the SC membrane in healthy and diseased states. We calculated key structural properties including the thickness, normalized lipid area, lipid tail order parameters, and spatial ordering of the lipids from each system. The results showed that systems with higher ordering and structural integrity contained an equimolar ratio of ceramides (chain length of 24 carbon atoms), fatty acids with chain lengths ≥ of 20 carbon atoms, and cholesterol. In these systems, strong apolar interactions between the ceramide and fatty acid long acyl chains restricted the mobility of the lipid molecules, thereby maintaining a compact lipid headgroup region and high order in the lipid tail region. The simulations also revealed distinct flip-flop mechanisms for cholesterol and fatty acid within the multi-layered membrane. Cholesterol is mostly diffused through the tail-tail interface region of the membrane and could flip-flop in the same bilayer. In contrast, fatty acids flip-flopped between adjacent leaflets of two bilayers in which the tails crossed the thinner headgroup region of the membrane. To conclude, our SC model provides mechanistic insights into lipid mobility and is flexible in its design and composition of different lipids, enabling studies of varying skin conditions.

The phase behavior of skin-barrier lipids: A combined approach of experiments and simulations

Skin barrier function is localized in its outermost layer, the stratum corneum (SC), which is comprised of corneocyte cells embedded in an extracellular lipid matrix containing ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs). The unique structure and composition of this lipid matrix are important for skin barrier function. In this study, experiments and molecular dynamics simulation were combined to investigate the structural properties and phase behavior of mixtures containing nonhydroxy sphingosine CER (CER NS), CHOL, and FFA. X-ray scattering for mixtures with varying CHOL levels revealed the presence of the 5.4 nm short periodicity phase in the presence of CHOL. Bilayers in coarse-grained multilayer simulations of the same compositions contained domains with thicknesses of approximately 5.3 and 5.8 nm that are associated with elevated levels, respectively, of CER sphingosine chains with CHOL, and CER acyl chains with FFA chains. The prevalence of the thicker domain increased with decreasing CHOL content. This might correspond to a phase with ∼5.8 nm spacing observed by x-rays (other details unknown) in mixtures with lower CHOL content. Scissoring and stretching frequencies from Fourier transform infrared spectroscopy (FTIR) also indicate interaction between FFA and CER acyl chains and little interaction between CER acyl and CER sphingosine chains, which requires CER molecules to adopt a predominantly extended conformation. In the simulated systems, neighbor preferences of extended CER chains align more closely with the FTIR observations than those of CERs with hairpin ceramide chains. Both FTIR and atomistic simulations of reverse mapped multilayer membranes detect a hexagonal to fluid phase transition between 65 and 80°C. These results demonstrate the utility of a collaborative experimental and simulation effort in gaining a more comprehensive understanding of SC lipid membranes.

Mechanisms of penetration and diffusion of drugs and cosmetic actives across the human Stratum corneum

Based on the structure of the Stratum corneum (SC) the potential penetration/diffusion pathways of drugs and cosmetic actives through the SC are presented and discussed. The well-known lipophilic pathway across the SC is presented and relevant examples are used to show that highly lipophilic molecules such as glucocorticoids, coenzyme Q10 etc. are accumulated in the SC and penetrate into the inner liquid like layer of the SC lipid bilayer by lateral diffusion. The diffusion into and across the SC of highly hydrophilic drugs and active substances such as urea, amino acids and peptides is still under discussion. Another diffusion pathway for the highly hydrophilic molecules via the corneocytes and the corneodesmosomes is presented and discussed, the corneocytary diffusion pathway.

Molecular Dynamics Investigation into CerENP's Effect on the Lipid Matrix of Stratum Corneum

The extracellular lipid matrix in the stratum corneum (SC) plays a critical role in skin barrier functionality, comprising three primary components: ceramides, cholesterol, and free fatty acids. The diverse ceramides, differentiated by molecular structures such as hydroxylations and varying chain lengths, are essential for the lipid matrix's structural integrity. Recently, a new subclass of ceramide, 1-O-acylceramide NP (CerENP), has been identified; however, its precise role in the lipid matrix of the SC is still elusive. Herein, we investigate the role of CerENP on the structure and permeability of the SC using molecular dynamics simulations. Our findings indicate that CerENP contributes to a compact lipid matrix in the lateral dimension of our SC model with a repeat distance of about 13 nm. Additionally, ethanol permeability assessments show that CerENP effectively reduces molecular penetration through the lipid matrix. This study provides an insight into the role of a new subclass of ceramide in the SC, enhancing our understanding of skin structure and the mechanisms behind barrier dysfunction in skin diseases.

Mechanisms of the Drug Penetration Enhancer Propylene Glycol Interacting with Skin Lipid Membranes

Very few drugs have the necessary physicochemical properties to cross the skin's main permeability barrier, the stratum corneum (SC), in sufficient amounts. Propylene glycol (PG) is a chemical penetration enhancer that could be included in topical formulations in order to overcome the barrier properties of the skin and facilitate the transport of drugs across it. Experiments have demonstrated that PG increases the mobility and disorder of SC lipids and may extract cholesterol from the SC, but little is known about the molecular mechanisms of drug permeation enhancement by PG. In this work, we have performed molecular dynamics (MD) simulations to investigate the molecular-level effects of PG on the structure and properties of model SC lipid bilayers. The model bilayers were simulated in the presence of PG concentrations over the range of 0-100% w/w PG, using both an all-atom and a united atom force field. PG was found to localize in the hydrophilic headgroup regions at the bilayer interface, to occupy the lipid-water hydrogen-bonding sites, and to slightly increase lipid tail disorder in a concentration-dependent manner. We showed with MD simulation that PG enhances the permeation of small molecules such as water by interacting with the bilayer interface; the results of our study may be used to guide the design of formulations for transdermal drug delivery with enhanced skin permeation, as well as topical formulations and cosmetic products.

Unraveling the Molecular Mechanisms of Alcohol-Mediated Skin Permeation Enhancement: Insights from Molecular Dynamics Simulations

The application of alcohols as permeation enhancers in pharmaceutical and cosmetic formulations has attracted considerable attention, owing to their skin permeation-enhancing effect. Nonetheless, the elucidation of the fundamental mechanisms underlying the skin permeation-enhancing effect remains elusive. In this study, molecular dynamics (MD) simulations were employed to investigate the effect of 1,2-propanediol (1,2-PDO), 1,2-butanediol (1,2-BDO), and ethanol (EtOH) on the stratum corneum (SC) model membrane. The results showed that the effect of alcohols on the SC model membrane displayed a concentration-dependent nature. The alcohols can interact with SC lipids and exhibit a remarkable ability to selectively extract free fatty acid (FFA) molecules from the SC model membrane and make the SC looser. Meanwhile, 1,2-BDO and EtOH can penetrate into SC lipid bilayers at higher concentrations, leading to the formation of continuous hydrophilic defects in SC. The FFA extraction and the formation of continuous hydrophilic defects induced ceramide (CER) tail chains to become more disordered and fluid and also weakened the hydrogen bonding (H-bonding) network among SC lipids. Both the FFA extraction and the continuous hydrophilic defect formation endowed alcohols with the permeation-enhancing effect. The constrained simulations revealed that the free energy barriers decreased for the permeation of the hydrophilic model molecule (COL) across the SC model membranes containing alcohols, particularly for 1,2-BDO and EtOH. The possible permeation-enhancing mechanisms of alcohols were proposed correspondingly. This work not only provided a deep understanding of the transdermal permeation-enhancing behavior of alcohols at the molecular level but also provided necessary reference information for designing effective transdermal drug delivery systems in applications.

The heterogeneity and complexity of skin surface lipids in human skin health and disease

The outermost epidermal layer of the skin, the stratum corneum, is not simply a barrier that safeguards skin integrity from external insults and invaders, it is also a delicately integrated interface composed of firm, essentially dead corneocytes and a distinctive lipid matrix. Together, the stratum corneum lipid matrix and sebum lipids derived from sebaceous glands give rise to a remarkably complex but quite unique blend of skin surface lipids that demonstrates tremendous heterogeneity and provides the skin with its indispensable protective coating. The stratum corneum lipid matrix is composed primarily of three major lipid classes: ceramides, non-esterified fatty acids and cholesterol, whereas sebum is a waxy mixture predominantly composed of acylglycerols, wax esters, non-esterified fatty acids, squalene, cholesterol and cholesterol esters. The balance of these skin surface lipids in terms of their relative abundance, composition, molecular organisation and dynamics, and their intricate interactions play a crucial role in the maintenance of healthy skin. For that reason, even minuscule alterations in skin surface lipid properties or overall lipid profile have been implicated in the aetiology of many common skin diseases including atopic dermatitis, psoriasis, xerosis, ichthyosis and acne. Novel lipid-based interventions aimed at correcting the skin surface lipid abnormalities have the potential to repair skin barrier integrity and the symptoms associated with such skin diseases, even though the exact mechanisms of lipid restoration remain elusive.

Investigation of β-caryophyllene as terpene penetration enhancer: Role of stratum corneum retention

Terpenes are usually used as penetration enhancers (PE) for transdermal drug delivery (TDD) of various molecules. However, TDD of hydrophilic macromolecules is becoming an urgent challenge due to their potent activities. The aim of this study was to investigate the potential application of β-caryophyllene (β-CP), a sequiterpene, as PE for TDD of hydrophilic macromolecules for the first time. Commonly used PEs, namely azone and 1,8-cineole (1,8-CN), were applied as controls. Transepidermal water loss (TEWL) analysis revealed that the reduction of skin barrier function caused by β-CP was reversible. Transdermal experiments showed that when skin was treated with β-CP or azone, there was a significant permeation-enhancing effect on fluorescein isothiocyanate (FITC) and FITC-dextran with different molecular weight (MW) of 4k or 10k. CLSM analysis confirmed that β-CP and azone can facilitate the penetration of FD-4k through epidermis and dermis. However, the cytotoxicity of azone against epidermal keratinocytes was significantly higher than β-CP and 1,8-CN. Additionally, application of β-CP and 1,8-CN didn't increase erythema index (EI) but the EI values of azone group increased significantly and irreversibly, indicating the high biocompatibility of the natural terpenes. β-CP had better permeation-enhancing effect and higher stratum corneum (SC) retention than 1,8-CN due to its increased carbon chain length and lipophilicity, as further demonstrated by molecular dynamics (MD) simulation studies. Skin electrical resistance (SER) and attenuated total reflection fourier transform infrared spectroscopy (ATR-FTIR) studies revealed a significant interfering effect of β-CP on SC lipids. Taken together, β-CP exhibited significant penetration enhancement of hydrophilic macromolecules due to its SC retention and SC lipid fluidization ability.

In Silico Prediction of Stratum Corneum Partition Coefficients via COSMOmic and Molecular Dynamics Simulations

Stratum corneum (SC) is the main barrier of human skin where the inter-corneocytes lipids provide the main pathway for transdermal permeation of functional actives of skin care and health. Molecular dynamics (MD) has been increasingly used to simulate the SC lipid bilayer structure so that the barrier property and its affecting factors can be elucidated. Among reported MD simulation studies, solute partition in the SC lipids, an important parameter affecting SC permeability, has received limited attention. In this work, we combine MD simulation with COSMOmic to predict the partition coefficients of dermatologically relevant solutes in SC lipid bilayer. Firstly, we run MD simulations to obtain equilibrated SC lipid bilayers with different lipid types, compositions, and structures. Then, the simulated SC lipid bilayer structures are fed to COSMOmic to calculate the partition coefficients of the solutes. The results show that lipid types and bilayer geometries play a minor role in the predicted partition coefficients. For the more lipophilic solutes, the predicted results of solute partition in SC lipid bilayers agree well with reported experimental values of solute partition in extracted SC lipids. For the more hydrophilic molecules, there is a systematical underprediction. Nevertheless, the MD/COSMOmic approach correctly reproduces the phenomenological correlation between the SC lipid/water partition coefficients and the octanol/water partition coefficients. Overall, the results show that the MD/COSMOmic approach is a fast and valid method for predicting solute partitioning into SC lipids and hence supporting the assessment of percutaneous absorption of skin care ingredients, dermatological drugs as well as environmental pollutants.

Formulation and Skin Permeation of Active-Loaded Lipid Nanoparticles: Evaluation and Screening by Synergizing Molecular Dynamics Simulations and Experiments

Encapsulation into nanoparticles (NPs) is a potential method to deliver pharmaceutical/cosmetic actives deep into the skin. However, understanding the NP formulations and underlying mechanism of active delivery to skin has scarcely been studied. We report a simulation platform that screens, evaluates, formulates, and provides atomic-resolution interpretation of NP-based formulations, and reveals the active permeation mechanism from NPs to skin. First, three actives, namely, ferulic acid (FA), clotrimazole (CZE), and tretinoin (TTN), and five lipid excipients' (Compritol, Precirol, Geleol, Gelot, Gelucire) combinations were screened by MD simulations for the best pairs. For each suggested pair, the actual active and lipid compositions for the synthesis of stable NP formulations were then obtained by experiments. MD simulations demonstrate that in NP formulations, FA and CZE actives are present at the surface of the NPs, whereas TTN actives are present at both the surface and interior of the NP core. The NP shapes obtained by simulation perfectly match with experiments. For each NP, separate MD simulations illustrate that active-loaded NPs approach the skin surface quickly, and then actives translocate from NP surface to skin surface followed by penetration of NPs through skin. The driving force for the translocation which initiates during the penetration process, is the stronger active-skin interaction compared to active-NP interaction. Permeation free energy indicates spontaneous transfer of actives from solution phase to the surface of the skin bilayer. The free energy barriers are increased in the order of FA < TTN < CZE. Significantly lower diffusions of actives are obtained in the main barrier region compared to bulk, and the average diffusion coefficients of actives are in the same order of magnitude (∼10^-6 cm²/s). The estimated permeability coefficients (log P) of actives are mainly governed by free energy barriers. The study would facilitate the development of novel lipid-based NP formulations for personal-care/pharmaceutical applications.

Effect of the CER[NP]:CER[AP] a ratio on the structure of a stratum corneum model lipid matrix - a molecular dynamics study

In some dermal diseases with evident skin dehydration and desquamation, the natural ratio of CER[NP]:CER[AP] is altered in the extracellular matrix of the stratum corneum by increasing the concentration of CER[AP]. The extracellular matrix of the stratum corneum is composed of several stacked lipid bilayers. Molecular dynamics simulations were used to investigate the molecular nanostructure of CER[NP], CER[AP], cholesterol and lignoceric acid models of the extracellular matrix of the stratum corneum with a nativelike CER[NP]:CER[AP] 2:1 ratio and a CER[NP]:CER[AP] ratio of 1:2. Despite the very minor chemical difference between CER[NP] and CER[AP], which is only a single OH group, it was possible to observe differences between the structural influence of the two ceramides. In the models with 1:2 ratio, the higher CER[AP] content leads to a larger inclination of the acyl chains and a smaller overlap in the lamellar midplane, with a small increase of the repeat distance compared to the model with higher CER[NP] concentration. Because CER[AP] forms more H-bonds than CER[NP], the total number of hydrogen bonds in the headgroup region is larger in the models with higher CER[AP] concentration, reducing the mobility of the lipids towards the centre of the bilayer and resulting in less overlap and increased tilt angles.

Molecular dynamics simulations of the human ocular lens with age and cataract

The human ocular lens consists primarily of elongated, static fibers characterized by high stability and low turnover, which differ dramatically in their composition and properties from other biological membranes. Cholesterol (Chol) and sphingolipids (SL) are present at high concentrations, including saturated SLs, such as dihyrosphingomyelin (DHSM). Past molecular dynamics simulations demonstrated that the presence of DHSM and high Chol concentration contributes to higher order in lipid membranes. This current study simulated more complex models of human lens membranes. Models were developed representing physiological compositions in cataractous lenses aged 74 ± 6 years and in healthy lenses aged 22 ± 4, 41 ± 6, and 69 ± 3 years. With older age, Chol and ceramide concentrations increase and glycerophospholipid concentration decreases. With cataract, ceramide concentration increases and Chol and glycerophospholipid concentrations decrease. Surface area per lipid, deuterium order parameters (S_CD), sterol tilt angle, electron density profiles, bilayer thickness, chain interdigitation, two-dimensional radial distribution functions (2D-RDF), lipid clustering, and hydrogen bonding were calculated for all simulations. All systems exhibited low surface area per lipid and high bilayer thickness, indicative of strong vertical packing. S_CD parameters suggest similarly, with saturated tails in the hydrophobic core of the membrane having elevated order. Vertical packing and acyl tail order increased with both age and cataract condition. Lateral diffusion decreased with age and cataracts, with the older and cataractous models demonstrating increased long-range structure by the 2D-RDF analysis. In future work examining the membrane proteins of the lens, these models can serve as a physiologically accurate representation of the lens lipidome.

Investigating the nanostructure of a CER[NP]/CER[AP]-based stratum corneum lipid matrix model: A combined neutron diffraction & molecular dynamics simulations approach

The human skin provides a physiochemical and biological protective barrier due to the unique structure of its outermost layer known as the Stratum corneum. This layer consists of corneocytes and a multi-lamellar lipid matrix forming a composite, which is a major determining factor for the barrier function of the Stratum corneum. A substantiated understanding of this barrier is necessary, as controlled breaching or modulation of the same is also essential for various health and personal care applications such as topical drug delivery and cosmetics to a name few. In this study, we discuss the state-of-the-art of neutron diffraction techniques, using specifically deuterated lipids, combined with the information obtained from molecular models using molecular dynamics simulations, to understand the structure and barrier function of the Stratum corneum lipid matrix. As an example, the effect of ceramide concentration on a lipid lamella system consisting of CER[NP]/CER[AP]/Cholesterol/free fatty acid (deprotonated) is studied. This study demonstrates the usefulness of the combined approach of neutron diffraction and molecular dynamics simulations for effective analysis of the model systems created for the Stratum corneum lipid matrix. The optimization of force fields by comparison with experimental data is furthermore an important step in the direction of providing a predictive quality.

Capturing the Liquid-Crystalline Phase Transformation: Implications for Protein Targeting to Sterol Ester-Rich Lipid Droplets

Lipid droplets are essential organelles that store and traffic neutral lipids. The phospholipid monolayer surrounding their neutral lipid core engages with a highly dynamic proteome that changes according to cellular and metabolic conditions. Recent work has demonstrated that when the abundance of sterol esters increases above a critical concentration, such as under conditions of starvation or high LDL exposure, the lipid droplet core can undergo an amorphous to liquid-crystalline phase transformation. Herein, we study the consequences of this transformation on the physical properties of lipid droplets that are thought to regulate protein association. Using simulations of different sterol-ester concentrations, we have captured the liquid-crystalline phase transformation at the molecular level, highlighting the alignment of sterol esters in alternating orientations to form concentric layers. We demonstrate how ordering in the core permeates into the neutral lipid/phospholipid interface, changing the magnitude and nature of neutral lipid intercalation and inducing ordering in the phospholipid monolayer. Increased phospholipid packing is concomitant with altered surface properties, including smaller area per phospholipid and substantially reduced packing defects. Additionally, the ordering of sterol esters in the core causes less hydration in more ordered regions. We discuss these findings in the context of their expected consequences for preferential protein recruitment to lipid droplets under different metabolic conditions.

Using molecular simulation to understand the skin barrier

Skin's effectiveness as a barrier to permeation of water and other chemicals rests almost entirely in the outermost layer of the epidermis, the stratum corneum (SC), which consists of layers of corneocytes surrounded by highly organized lipid lamellae. As the only continuous path through the SC, transdermal permeation necessarily involves diffusion through these lipid layers. The role of the SC as a protective barrier is supported by its exceptional lipid composition consisting of ceramides (CERs), cholesterol (CHOL), and free fatty acids (FFAs) and the complete absence of phospholipids, which are present in most biological membranes. Molecular simulation, which provides molecular level detail of lipid configurations that can be connected with barrier function, has become a popular tool for studying SC lipid systems. We review this ever-increasing body of literature with the goals of (1) enabling the experimental skin community to understand, interpret and use the information generated from the simulations, (2) providing simulation experts with a solid background in the chemistry of SC lipids including the composition, structure and organization, and barrier function, and (3) presenting a state of the art picture of the field of SC lipid simulations, highlighting the difficulties and best practices for studying these systems, to encourage the generation of robust reproducible studies in the future. This review describes molecular simulation methodology and then critically examines results derived from simulations using atomistic and then coarse-grained models.

Phosphatidylserine and Phosphatidylethanolamine Asymmetry Have a Negligible Effect on the Global Structure, Dynamics, and Interactions of the KRAS Lipid Anchor

The intrinsically disordered C-terminus of the prominent oncogenic protein KRAS-4B (KRAS) selectively interacts and clusters with phosphatidylserine (PS) lipids in the plasma membrane (PM). This 11-residue segment, called tK, contains a polybasic domain (PBD) of six contiguous lysine residues and a farnesylated cysteine. Previous molecular dynamics (MD) simulation studies of tK in phosphatidylcholine (PC)/PS bilayers have suggested that backbone conformational dynamics modulate tK-PS interactions. These simulations have been conducted in symmetric membranes whereas the PM is compositionally asymmetric, with the inner leaflet, where KRAS is localized, being enriched with PS and phosphatidylethanolamine (PE) lipids. To examine if bilayer asymmetry affects tK conformational dynamics and interaction with lipids, we conducted two 10 μs long MD simulations of tK bound to a PC/PS and a PC/PS/PE bilayer in which the PS and PE lipids are distributed in one leaflet. We found that, first, these compositional asymmetries caused differences in acyl chain dynamics between leaflets, but the equilibrium structural and dynamic properties of the two asymmetric bilayers are similar; second, in both systems tK is highly dynamic and samples at least two distinct conformational states; third, PS-tK hydrogen-bonding interactions vary with peptide backbone conformations, and lysine side chains in the PBD predominantly interact with the serine oxygens of PS. These results are in good agreement with previous observations of tK in symmetric membranes. The effects of POPS asymmetry or the presence of POPE on tK are limited to modulating the relative contribution of individual side chains to interactions with lipids and redistributing conformational substates. Additional observations include the larger flexibility of tK in the current simulations, which we attribute to the longer duration of the simulations and the use of the CHARMM36m force field, which more accurately models intrinsically disordered peptides such as tK.

Multiscale Simulation of Ternary Stratum Corneum Lipid Mixtures: Effects of Cholesterol Composition

Molecular dynamics simulations of mixtures of the ceramide nonhydroxy-sphingosine (NS), cholesterol, and a free fatty acid are performed to gain molecular-level understanding of the structure of the lipids found in the stratum corneum layer of skin. A new coarse-grained force field for cholesterol was developed using the multistate iterative Boltzmann inversion (MS-IBI) method. The coarse-grained cholesterol force field is compatible with previously developed coarse-grained force fields for ceramide NS, free fatty acids, and water and validated against atomistic simulations of these lipids using the CHARMM force field. Self-assembly simulations of multilayer structures using these coarse-grained force fields are performed, revealing that a large fraction of the ceramides adopt extended conformations, which cannot occur in the single bilayer in water structures typically studied using molecular simulation. Cholesterol fluidizes the membrane by promoting packing defects, and an increase in cholesterol content is found to reduce the bilayer thickness due to an increase in interdigitation of the C₂₄ lipid tails, consistent with experimental observations. Using a reverse-mapping procedure, a self-assembled coarse-grained multilayer system is used to construct an equivalent structure with atomistic resolution. Simulations of this atomistic structure are found to closely agree with experimentally derived neutron scattering length density profiles. Significant interlayer hydrogen bonding is observed in the inner layers of the atomistic multilayer structure that are not found in the outer layers in contact with water or in equivalent bilayer structures. This work highlights the importance of simulating multilayer structures, as compared to the more commonly studied bilayer systems, to enable more appropriate comparisons with multilayer experimental membranes. These results also provide validation of the efficacy of the MS-IBI derived coarse-grained force fields and the framework for multiscale simulation.

All-Atom Modeling of Complex Cellular Membranes

Cell membranes are composed of a variety of lipids and proteins where they interact with each other to fulfill their roles. The first step in modeling these interactions in molecular simulations is to have reliable mimetics of the membrane's lipid environment. This Feature Article presents our recent efforts to model complex cellular membranes using all-atom force fields. A short review of the CHARMM36 (C36) lipid force field and its recent update to incorporate the long-range dispersion is presented. Key examples of model membranes mimicking various species and organelles are given. These include single-celled organisms such as bacteria (E. coli., chlamydia, and P. aeruginosa) and yeast (plasma membrane, endoplasmic reticulum, and trans-Golgi network) and more advanced ones such as plants (soybean and Arabidopsis thaliana) and mammals (ocular lens, stratum corneum, and peripheral nerve myelin). Leaflet asymmetry in composition has also been applied to some of these models. With the increased lipid diversity in the C36 lipid FF, these complex models can better reflect the structural, mechanical, and dynamic properties of realistic membranes and open an opportunity to study biological processes involving other molecules.

Leaflet Asymmetry Modeling in the Lipid Composition of Escherichia coli Cytoplasmic Membranes

Lipid composition asymmetry between leaflets is important to cell function and plays a key role in the "positive inside" rule in transmembrane proteins. In this work, Escherichia coli inner plasma membrane models reflecting this asymmetry have been investigated at the early-log and stationary stages during the bacterial lifecycle using all-atom molecular dynamics simulations. The CHARMM36 lipid force field is used, and selected membrane properties are tested for variations between two leaflets and whole membranes. Our models include bacterial lipids with a cyclopropane moiety on the sn-2 acyl chain in the stationary membrane model. The PE/PG ratio for two leaflets reflects the "positive inside" rule of membrane proteins, set to 6.8 and 2.8 for the inner and outer leaflets of the two models, respectively. We are the first to model leaflet asymmetry in the lipid composition of E. coli cytoplasmic membranes and observe the effect on membrane properties in leaflets and whole membranes. Specifically, our results show that for the stationary phase bilayer, the surface area per lipid (SA/lipid) is larger, the thickness (2D_C and D_B) is smaller, the tilt angle is larger, the tilt modulus is smaller, and the deuterium order parameters (S_CD) of sn-1 and sn-2 tails are lower, compared to the early-log stage. Moreover, the stationary stage bilayer has a positive spontaneous curvature, while the early-log stage has a near flat spontaneous curvature. For leaflet asymmetry, the inner leaflet has a larger SA/lipid, a smaller thickness, a smaller elastic tilt modulus (a larger tilt angle), and lower S_CD, compared to the outer leaflet in both stages. Moreover, an asymmetric membrane involves a lipid tilt and a lateral extension, varying from a reference state of a pre-equilibrium membrane. This work encourages a more profound exploration of leaflet asymmetry in various other membrane models and how this might affect the structure and function of membrane-associated peptides and proteins.

Evaluation of Constrained and Restrained Molecular Dynamics Simulation Methods for Predicting Skin Lipid Permeability

Recently, molecular dynamics (MD) simulations have been utilized to investigate the barrier properties of human skin stratum corneum (SC) lipid bilayers. Different MD methods and force fields have been utilized, with predicted permeabilities varying by few orders of magnitude. In this work, we compare constrained MD simulations with restrained MD simulations to obtain the potential of the mean force and the diffusion coefficient profile for the case of a water molecule permeating across an SC lipid bilayer. Corresponding permeabilities of the simulated lipid bilayer are calculated via the inhomogeneous solubility diffusion model. Results show that both methods perform similarly, but restrained MD simulations have proven to be the more robust approach for predicting the potential of the mean force profile. Critical to both methods are the sampling of the whole trans-bilayer axis and the following symmetrization process. Re-analysis of the previously reported free energy profiles showed that some of the discrepancies in the reported permeability values is due to misquotation of units, while some are due to the inaccurately obtained potential of the mean force. By using the existing microscopic geometrical models via the intercellular lipid pathway, the permeation through the whole SC is predicted from the MD simulation results, and the predicted barrier properties have been compared to experimental data from the literature with good agreement.

Ion-Pair Compounds of Strychnine for Enhancing Skin Permeability: Influencing the Transdermal Processes In Vitro Based on Molecular Simulation

This research aimed to explore how Strychnine (Str) ion-pair compounds affect the in vitro transdermal process. In order to prevent the influence of different functional groups on skin permeation, seven homologous fatty acids were selected to form ion-pair compounds with Str. The in vitro permeation fluxes of the Str ion-pair compounds were 2.2 to 8.4 times that of Str, and Str-C₁₀ had the highest permeation fluxes of 42.79 ± 19.86 µg/cm²/h. The hydrogen bond of the Str ion-pair compounds was also confirmed by Fourier Transform Infrared (FTIR) Spectroscopy, Nuclear Magnetic Resonance (NMR) Spectroscopy and molecular simulation. In the process of molecular simulation, the intercellular lipid and the viable skin were represented by ceramide, cholesterol and free fatty acid of equal molar ratios and water, respectively. It was found by the binding energy curve that the Str ion-pair compounds had better compatibility with the intercellular lipid and water than Str, which indicated that the affinity of Str ion-pair compounds and skin was better than that of Str and skin. Therefore, it was concluded that Str ion-pair compounds can be distributed from the vehicle to the intercellular lipid and viable skin more easily than Str. These findings broadened our knowledge about how Str ion-pair compounds affect the transdermal process.

Mechanistic Insight on BioIL-Induced Structural Alterations in DMPC Lipid Bilayer

The emerging application risks of traditional ionic liquids (ILs) toward the ecosystem have changed the perception regarding their greenness. This resulted in the exploration of their more biocompatible alternatives known as biocompatible ILs (BioILs). Here, we have investigated the impact of two such biocompatible cholinium amino acid-based ILs on the structural behavior of model homogeneous DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) lipid bilayer using all-atom molecular dynamics simulation technique. Two classic cholinium-amino acid-based ILs, cholinium glycinate ([Ch][Gly]) and cholinium phenylalaninate ([Ch][Phe]), which differ only by the side chain lengths and hydrophobicity of the anions, have been utilized in the present work. Simultaneous analysis of the bilayer structural properties reveals that the existence of [Ch][Gly] BioIL above a particular concentration induces phase transition from fluid phase to gel phase in the DMPC lipid bilayer. Such a freezing of lipid bilayer upon the exposure to concentrated aqueous solution of [Ch][Gly] BioIL indicates the harmfulness of this BioIL toward the cell membranes majorly containing DMPC lipids, as the cell freezing can negatively affect its stability and functionality. Despite having a more hydrophobic amino acid side chain of [Phe]^- anion in [Ch][Phe], in the case of bilayer-[Ch][Phe] systems we observe the minimal impact of [Ch][Phe] BioIL on the DMPC bilayer properties up to 10 mol % concentration. In the presence of these BioIL, we observe the thickening of the bilayer and accumulation of the cations and anions of the BioILs at the interface of DMPC lipid heads and tails. The transfer free-energy profile of a [Phe]^- anion from aqueous phase to membrane center also indicates the anion partitioning at lipid head-tail interface and its inability to penetrate in the lipid membrane tail region. In contrast, the free-energy profile for a [Gly]^- anion offers a very high energy barrier to the insertion of [Gly]^- into the membrane interior, leading to accumulation of [Gly]^- anions at the lipid head-water region.

Interaction between SARS-CoV-2 spike glycoprotein and human skin models: a molecular dynamics study

The possibility of contamination of human skin by infectious virions plays an important role in indirect transmission of respiratory viruses but little is known about the fundamental physico-chemical aspects of the virus-skin interactions. In the case of coronaviruses, the interaction with surfaces (including the skin surface) is mediated by their large glycoprotein spikes that protrude from (and cover) the viral envelope. Here, we perform all atomic simulations between the SARS-CoV-2 spike glycoprotein and human skin models. We consider an "oily" skin covered by sebum and a "clean" skin exposing the stratum corneum. The simulations show that the spike tries to maximize the contacts with stratum corneum lipids, particularly ceramides, with substantial hydrogen bonding. In the case of "oily" skin, the spike is able to retain its structure, orientation and hydration over sebum with little interaction with sebum components. Comparison of these results with our previous simulations of the interaction of SARS-CoV-2 spike with hydrophilic and hydrophobic solid surfaces, suggests that the "soft" or "hard" nature of the surface plays an essential role in the interaction of the spike protein with materials.

Symmetric and Asymmetric Models for the Arabidopsis thaliana Plasma Membrane: A Simulation Study

Arabidopsis thaliana is an important model organism, which has attracted many biologists. While most research efforts have been on studying the genetics and proteins of this organism, a systematic study of its lipidomics is lacking. Here, we present a novel, asymmetric model of its cell membrane with its lipid composition consisting of five glycerophospholipids, two glycolipids, and sitosterol determined from multiple independent experiments. A typical lipid type in plant membranes is glycosyl inositol phosphoryl ceramide (GIPC), which accounts for about 10% of the total lipids in the outer leaflet in our model. Two symmetric models representing the inner and outer leaflets of the membrane were built and simulated until equilibrium was reached and then combined to form the asymmetric model. Our results indicate that the outer leaflet is more rigid and tightly packed compared to the inner leaflet. Pressure profiles for the two leaflets are overall similar though the outer leaflet exhibits larger oscillations. A special focus on lipid organization is discussed and the interplay between glycolipids and sitosterols is found to be important. The current model provides a baseline for future modeling of similar membranes and can be used to study partitioning of small molecules in the membrane or further developed to study the interaction between plant membrane proteins and lipids.

Topical drug delivery: History, percutaneous absorption, and product development

Topical products, widely used to manage skin conditions, have evolved from simple potions to sophisticated delivery systems. Their development has been facilitated by advances in percutaneous absorption and product design based on an increasingly mechanistic understanding of drug-product-skin interactions, associated experiments, and a quality-by-design framework. Topical drug delivery involves drug transport from a product on the skin to a local target site and then clearance by diffusion, metabolism, and the dermal circulation to the rest of the body and deeper tissues. Insights have been provided by Quantitative Structure Permeability Relationships (QSPR), molecular dynamics simulations, and dermal Physiologically Based PharmacoKinetics (PBPK). Currently, generic product equivalents of reference-listed products dominate the topical delivery market. There is an increasing regulatory interest in understanding topical product delivery behavior under 'in use' conditions and predicting in vivo response for population variations in skin barrier function and response using in silico and in vitro findings.

Molecular dynamics simulations to elucidate translocation and permeation of active from lipid nanoparticle to skin: complemented by experiments

One of the most realistic approaches for delivering actives (pharmaceuticals/cosmetics) deep into skin layers is encapsulation into nanoparticles (NPs). Nonetheless, molecular-level mechanisms related to active delivery from NPs to the skin have scarcely been studied despite the large number of synthesis and characterization studies. We herein report the underlying mechanism of active translocation and permeation through the outermost layer of skin, the stratum corneum (SC), via molecular dynamics (MD) simulations complemented by experimental studies. A SC molecular model is constructed using current state-of-the-art methodology via incorporating the three most abundant skin lipids: ceramides, free fatty acids, and cholesterol. As a potent antioxidant, ferulic acid (FA) is used as the model active, and it is loaded into Gelucire 50/13 NP. MD simulations elucidate that, first, FA-loaded NP approaches the skin surface quickly, followed by slight penetration and adsorption onto the upper skin surface; FA then translocates from the NP surface to the skin surface due to stronger NP-skin interactions compared to the FA-NP interactions; then, once FA is released onto the skin surface, it slowly permeates deep into the skin bilayer. Both the free energy and resistance to permeation not only indicate the spontaneous transfer of FA from the bulk to the skin surface, but they also reveal that the main barrier against permeation exists in the middle of the lipid hydrophobic tails. Significantly lower diffusion of FA is obtained in the main barrier region compared to the bulk. The estimated permeability coefficient (log P) values are found to be higher than the experimental values. Importantly, the permeation process evaluated via MD simulations perfectly matches with experiments. The study suggests a molecular simulation platform that provides various crucial insights relating to active delivery from loaded NP to skin, and it could facilitate the design and development of novel NP-based formulations for transdermal delivery and the topical application of drugs/cosmetics.

Simulations of Diabetic and Non-Diabetic Peripheral Nerve Myelin Lipid Bilayers

The multilayered myelin sheath is a critical component of both central and peripheral nervous systems, forming a protective barrier against axonal damage and facilitating the movement of nervous impulses. It is primarily composed of cholesterol (CHL1), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), sphingomyelin (SM), and galactosylceramide (GalCer) lipids. For rat sciatic nerve myelin (part of the peripheral nervous system, PNS), it has been found that cholesterol and unsaturated fatty acid contents are significantly lower in diabetic than in non-diabetic conditions. In this study, lipid compositions from experimental data are used to create four model rat sciatic nerve myelin lipid bilayers: PI-containing (non-diabetic and diabetic) and PS-containing (non-diabetic and diabetic), which were then simulated using the all-atom CHARMM36 force field. Simulation results of diabetic membranes indicate less rigid, more laterally expansive, and thinner bilayers as well as potentially reduced interactions between GalCer on opposing myelin leaflets, supporting a direct role of the cholesterol content decrease in instigating myelin deterioration and diabetic peripheral neuropathy. Compared to PI-lipids, PS-lipids were found to cause higher inter-lipid spacing and decreased order within membranes as a result of their smaller headgroup size and higher inter-lipid hydrogen bonding potential, which allow them to more frequently reside deeper in the membrane plane and produce pushing effects on other lipids. GalCer deuterium order parameters and non-diabetic headgroup-to-headgroup bilayer thicknesses were compared to experimental data, exhibiting close alignment, supporting the future usage of these models to study the PNS myelin sheath.

Synergistic Effect of Chemical Penetration Enhancers on Lidocaine Permeability Revealed by Coarse-Grained Molecular Dynamics Simulations

The search for new formulations for transdermal drug delivery (TDD) is an important field in medicine and cosmetology. Molecules with specific physicochemical properties which can increase the permeability of active ingredients across the stratum corneum (SC) are called chemical penetration enhancers (CPEs), and it was shown that some CPEs can act synergistically. In this study, we performed coarse-grained (CG) molecular dynamics (MD) simulations of the lidocaine delivery facilitated by two CPEs-linoleic acid (LA) and ethanol-through the SC model membrane containing cholesterol, N-Stearoylsphingosine (DCPE), and behenic acid. In our simulations, we probed the effects of individual CPEs as well as their combination on various properties of the SC membrane and the lidocaine penetration across it. We demonstrated that the addition of both CPEs decreases the membrane thickness and the order parameters of the DPCE hydrocarbon chains. Moreover, LA also enhances diffusion of the SC membrane components, especially cholesterol. The estimated potential of mean force (PMF) profiles for the lidocaine translocation across SC in the presence/absence of two individual CPEs and their combination demonstrated that while ethanol lowers the free energy barrier for lidocaine to enter SC, LA decreases the depth of the free energy minima for lidocaine inside SC. These two effects supposedly result in synergistic penetration enhancement of drugs. Altogether, the present simulations provide a detailed molecular picture of CPEs' action and their synergistic effect on the penetration of small molecular weight therapeutics that can be beneficial for the design of novel drug and cosmetics formulations.

The Surface and Hydration Properties of Lipid Droplets

Lipid droplets (LDs) are energy storage organelles composed of neutral lipids, such as triacylglycerol (TG) and sterol esters, surrounded by a phospholipid (PL) monolayer. Their central role in metabolism, complex life cycle, and unique lipid monolayer surface have garnered great attention over the last decade. In this article, results from the largest and longest all-atom simulations to date suggest that 5-8% of the LD surface is occupied by TG molecules, a number that exceeds the maximal solubility reported for TGs in PL bilayers (2.8%). Two distinct classes of TG molecules that interact with the LD monolayer are found. Those at the monolayer surface (SURF-TG) are ordered like PLs with the glycerol moiety exposed to water, creating a significant amount of chemically unique packing defects, and the acyl chains extended toward the LD center. In contrast, the TGs that intercalate just into the PL tail region (CORE-TG) are disordered and increase the amount of PL packing defects and the PL tail order. The degree of interdigitation caused by CORE-TG is stable and determines the width of the TG-PL overlap, whereas that caused by SURF-TG fluctuates and is highly correlated with the area per PL or the expansion of the monolayer. Thus, when the supply of PLs is limited, SURF-TG may reduce surface tension by behaving as a secondary membrane component. The hydration properties of the simulated LD systems demonstrate ∼10 times more water in the LD core than previously reported. Collectively, the reported surface and hydration properties are expected to play a direct role in the mechanisms by which proteins target and interact with LDs.

Arrangement of Ceramides in the Skin: Sphingosine Chains Localize at a Single Position in Stratum Corneum Lipid Matrix Models

Understanding the structure of the stratum corneum (SC) is essential to understand the skin barrier process. The long periodicity phase (LPP) is a unique trilayer lamellar structure located in the SC. Adjustments in the composition of the lipid matrix, as in many skin abnormalities, can have severe effects on the lipid organization and barrier function. Although the location of individual lipid subclasses has been identified, the lipid conformation at these locations remains uncertain. Contrast variation experiments via small-angle neutron diffraction were used to investigate the conformation of ceramide (CER) N-(tetracosanoyl)-sphingosine (NS) within both simplistic and porcine mimicking LPP models. To identify the lipid conformation of the twin chain CER NS, the chains were individually deuterated, and their scattering length profiles were calculated to identify their locations in the LPP unit cell. In the repeating trilayer unit of the LPP, the acyl chain of CER NS was located in the central and outer layers, while the sphingosine chain was located exclusively in the middle of the outer layers. Thus, for the CER NS with the acyl chain in the central layer, this demonstrates an extended conformation. Electron density distribution profiles identified that the lipid structure remains consistent regardless of the lipid's lateral packing phase, this may be partially due to the anchoring of the extended CER NS. The presented results provide a more detailed insight on the internal arrangement of the LPP lipids and how they are expected to be arranged in healthy skin.

Molecular Dynamics Evaluation of the Effect of Cholinium Phenylalaninate Biocompatible Ionic Liquid on Biomimetic Membranes

Toward the search of sustainable green solvents, choline amino acid ([Ch][AA]) ionic liquids (ILs), mainly derived from renewable feedstocks, have emerged as a promising atoxic alternative to the conventional solvents. Recent studies have shown the remarkably benign nature of cholinium-based ILs against biomimetic phospholipid membranes. However, few of the contemporaneous experimental studies have contradicted the aforesaid ecofriendly nature of these ILs with anions comprising longer alkyl or aromatic tails. Aiming to understand the influence of amino acid side-chain variation in a particular bio-IL on biomembranes, herein, we have evaluated the effect of cholinium phenylalaninate ([Ch][Phe]) IL on the structural stability of homogeneous biomimetic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) lipid bilayers using atomistic molecular dynamics simulations. Although we observe spontaneous intercalation of aromatic rings of [Phe]^- anions in the hydrophobic region of the bilayers, the polar backbone of the anion remains coordinated with the lipid polar part through strong electrostatic and H-bonding interactions. Besides, the [Ch]⁺ cations get accumulated at the lipid-water interface to counter the excess negative charge density. The intercalation of the anionic rings causes significant perturbations in the lipid structural arrangement while still maintaining the bilayer integrity. The quantitative evaluation to probe the deteriorating effect of this bio-IL application establishes anions as the principal component causing the observed structural perturbations. The analysis of the structural properties along with the free energy assessment reveals the higher efficacy of [Ch][Phe] bio-IL to perturb the POPE bilayer structure than the POPC bilayer.

Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids

Accurate lipid force field (FF) parameters used in molecular dynamics (MD) simulations are crucial for understanding the properties of lipid-containing systems and biological processes related to lipids. The last update of the CHARMM36 united atom chain model (C36UA) was in 2013 [Lee, S. J. Phys. Chem. B 2014, 118, 547 556]; it utilized CHARMM36 (C36) lipid FF parameters for headgroups and OPLS-UA Lennard-Jones (LJ) parameters for tails. Simulations with the FF were able to reproduce many experimental observables of lipid bilayers accurately, but to be more applicable for a wide range of lipids, additional FF parameter optimization was needed. In this work, we present an update of the model, named C36UAr. The parameterization included the LJ parameters for hydrocarbons and related dihedrals. Bulk liquid properties (density, heat of vaporization, isothermal compressibility, and diffusion constant) of model compounds were used as targets for the LJ parameter fitting, and dihedrals were fit to either quantum mechanical (QM) or potential of mean force (PMF) calculations using C36. Thermodynamic reweighting was used to further improve the parameters. Bilayer simulations of various lipid headgroups (phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol) and tails (saturated, monounsaturated, and polyunsaturated) were performed to validate the model, and significant improvements were seen in bilayer properties, including surface area, membrane thicknesses, NMR deuterium order parameters, and density profiles. C36UAr was also compared to the hydrogen mass repartitioning (HMR) method. The high accuracy and competitive efficiency shown in this study make C36UAr one of the best choices for studies of membrane structure and membrane-associated proteins.

Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. I. Differences in physicochemical properties between the two leaflets

Outer and inner leaflets of plasma cell membranes have different lipid compositions, and the membrane properties of each leaflet can differ from each other significantly due to these composition differences. However, because of the experimental difficulty in measuring the membrane properties for each leaflet separately, the differences are not well understood at a molecular level. In this study, we constructed two lipid bilayer systems, modeling outer and inner leaflets of plasma membranes of mouse hepatocytes based on experimental composition data. The ion concentration in the interlamellar water phase was also set to match the concentration in extra- and intracellular fluids. The differences in physical properties between the outer and inner leaflets of mouse hepatocyte cell membrane models were investigated by performing 1.2 μs-long all-atomistic molecular dynamics calculations under physiological temperature and pressure conditions (310.15 K and 1 atm). The calculated electron density profiles along the bilayer normal for each model bilayer system captured well the asymmetric feature of the experimental electron density profile across actual cell plasma membranes, indicating that our procedure of modeling the outer and inner leaflets of the cell plasma membranes was satisfactory. We found that compared to the outer leaflet model, the inner leaflet model had a very bulky and soft structure in the lateral direction. To confirm the differences, membrane fluidity was measured from the lateral diffusivity and relaxation times. The fluidity was significantly higher in the inner leaflet model than in the outer leaflet model. We also discuss two topics that are of wide interest in biology, i.e., the interdigitation of acyl tails of lipid molecules between two monolayers and the lateral concentration fluctuation of lipid molecules in the bilayers.

State of the Art in Stratum Corneum Research. Part II: Hypothetical Stratum Corneum Lipid Matrix Models

This review is the second part of a series which presents the state of the art in stratum corneum (SC) lipid matrix (LM) research in depth. In this part, the various hypothetical models which were developed to describe the structure and function of the SC LM as the skin's barrier will be discussed. New as well as a cumulative assortment of older results which change the view on the different models are considered to conclude how well the different models are holding up today. As a final conclusion, a model, factoring in as much of the known data as possible, is concluded, unifying the varying different models into one which can be developed further, as new results are found in the future. So far, the model is described with a single crystalline or gel-like phase with a certain amount of nanocrystallites of concentrated ceramides (CERs) and free fatty acids and more fluid nanodomains caused by a fluidizing effect of the cholesterol. These domains are dynamically resolved and reformed and do not impair the barrier function. The chain conformation is not completely clear yet; however, an equilibrium of fully extended and hairpin-folded CERs with ratios depending on the properties of each individual CER species is proposed as most likely. An overlapping middle layer as described for the tri-layer model in part I of this series would be present for both conformations. The macroscopic broad-narrow-broad layering, observed in electron micrographs, is explained by an external templating by the lipid envelope, and an internal templating by short and long lipid chains each preferentially show a homophilic association, forming thicker and thinner bilayers, respectively. The degree of influence of the very long ω-hydroxy-CERs is discussed as well.

Molecular Dynamics Simulations of Micelle Properties and Behaviors of Sodium Lauryl Ether Sulfate Penetrating Ceramide and Phospholipid Bilayers

Molecular dynamics (MD) simulations with the umbrella sampling (US) method were used to investigate the properties of micelles formed by sodium lauryl ether sulfate with two ether groups (SLE2S) and behaviors of corresponding surfactants transferring from micelles to ceramide and DMPC bilayer surfaces. Average micelle radii based on the Einstein-Smoluchowski and Stokes-Einstein relations showed excellent agreement with those measured by dynamic light scattering, while those obtained by evaluating the gyration radius or calculating the distance between the micelle sulfur atoms and center of mass overestimate the radii. As an SLE2S micelle was pulled down to the ceramide bilayer surface in a 400 ns constant-force steered MD (cf-SMD) simulation, the micelle was partially deformed on the bilayer surface, and several SLE2S surfactants easily were partitioned from the micelle into the ceramide bilayer. In contrast, a micelle was not deformed on the DMPC bilayer surface, and SLE2S surfactants were not transferred from the micelle to the DMPC bilayer. Potential of mean force (PMF) calculations revealed that the Gibbs free energy required for an SLE2S surfactant monomer to transfer from a micelle to bulk water can be compensated by decreased Gibbs free energy when an SLE2S monomer transfers into the ceramide bilayer from bulk water. In addition, micelle deformation on the ceramide bilayer surface can reduce the Gibbs free energy barrier required for a surfactant to escape the micelle and help the surfactant partition from the micelle into the ceramide bilayer. An SLE2S surfactant partitioning into the ceramide bilayer is attributed to hydrogen bonding and favorable interactions between the hydrophilic surfactant head and ceramide molecules, which are more dominant than the dehydration penalty during bilayer insertion. Such interactions between surfactant and lipid molecule heads are considerably reduced in DMPC bilayers owing to dielectric screening by water molecules deep inside the head/tail boundary between the DMPC bilayer. This computational work demonstrates the distinct behavior of SLE2S surfactant micelles on ceramide and DMPC bilayer surfaces in terms of variation in Gibbs free energy, which offers insight into designing surfactants used in transdermal drug delivery systems and cosmetics.

Development and application of coarse-grained MARTINI model of skin lipid ceramide [AP]

Stratum corneum (SC), the outermost layer of the skin, contains large variety of lipids, endowing them with the amphiphilic properties, needed to fulfil their key role in skin's barrier function. The individual role of lipid types in the barrier function is difficult to understand due to the immense heterogeneity and complexity of the lipid's organization within the SC. The lipid organization is being explored using both computational (molecular dynamics simulations) and experimental (neutron diffraction) techniques. Even though atomistic simulations provide unprecedented atomic level details, the major limitation is time and length scale that can be achieved with decent computational facility. Alternatively, coarse-grain (CG) models are currently being used to capture physics at bigger time and length scale without losing essential underlined structural information. In this study, a CG model of α-hydroxy phytosphingosines (CER[AP]) is developed based on philosophy of MARTINI force field. At first, the model is validated with various atomistic simulations and available experimental data. Later on, the model's compatibility with other major skin lipids, cholesterol, and free fatty acid (palmitic acid) is checked by simulating a mixture of lipid multilayer in presence and absence of water. The developed model of CER[AP] is able to predict key structural properties within the acceptable error limits. The phenomena of ceramide conformation transformation, cholesterol flip-flop, and specificity of lipid arrangement within the multilayered systems is observed during the simulation. This signifies the importance of model in capturing higher order structural transformations.

Multiscale Modeling of Skin Electroporation

Human skin, the largest external organ of the body, provides a selective barrier to therapeutics applied topically. The molecules having specific chemical and physical properties can only penetrate the deeper layer of the skin. However, the lag time for reaching a steady state in the deeper layer is generally of the order of hours. In order to deliver higher-molecular-weight, charged, and hydrophilic therapeutics in the deeper layer, the skin barrier must be breached. Electroporation is one of the methods used to breach the skin barrier for enhancement of drug permeation and reduction of lag time. However, the underlying mechanism responsible for the enhancement of drug permeation is not well understood. In this study, a multiscale model of skin electroporation is developed by connecting molecular phenomena to a macroscopic model. At the atomic scale, molecular dynamics simulations of the lipid matrix of the human stratum corneum (SC) were performed under the influence of an external electric field. The pores get formed during the electroporation process and the transport properties (diffusivity) of drug molecules are computed. The diffusion coefficient obtained during electroporation was found to be higher than passive diffusion. However, this alone could not explain the multifold increase in the drug flux on application of an electric field as observed in the experiments. Hence, a finite element method (FEM) model of the skin SC is also developed. The release of fentanyl through this model is compared with the available experimental results. Both experimental and simulated results of pore formation on application of an electric field and many folds' increase in drug flux are comparable. Once validated, the framework was used for the design of skin electroporation experiments (in silico) by changing the electric pulse parameters such as voltage, pulse duration, and number of pulses. This multiscale modeling framework provides valuable insight at the molecular and macroscopic levels to design the electroporation experiments. The framework can be utilized as a design tool for skin electroporation applications.

Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes

Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.

Electric-field-induced electroporation and permeation of reactive oxygen species across a skin membrane

Electroporation processes affect the permeability of cell membranes, which can be utilized for the delivery of plasma species in cancer therapy. By means of computational dynamics, many aspects of membrane electroporation have been unveiled at the atomic level for lipid membranes. Herein, a molecular dynamics simulation study was performed on native and oxidized membrane systems with transversal electric fields. The simulation result shows that the applied electric field mainly affects the membrane properties so that electroporation takes place and these pores are lined by hydrophilic headgroups of the lipid components. The calculated hydrophobic thickness, lateral diffusion and pair correlation revealed the role of 5α-CH in creation of water-pore in an oxidized membrane. Additionally, the permeability of reactive oxygen species was examined through these electroporated systems. The permeability study suggested that water pores in the membrane facilitate the penetration of these species across the membrane to the interior of the cell. These findings may have significance in experimental applications in vivo as once the reactive oxygen species reaches the interior of the cell, they may cause oxidative stress and induce apoptosis.Communicated by Ramaswamy H. Sarma.

Effect of Ceramide Tail Length on the Structure of Model Stratum Corneum Lipid Bilayers

Lipid bilayers composed of non-hydroxy sphingosine ceramide (CER NS), cholesterol (CHOL), and free fatty acids (FFAs), which are components of the human skin barrier, are studied via molecular dynamics simulations. Since mixtures of these lipids exist in dense gel phases with little molecular mobility at physiological conditions, care must be taken to ensure that the simulations become decorrelated from the initial conditions. Thus, we propose and validate an equilibration protocol based on simulated tempering, in which the simulation takes a random walk through temperature space, allowing the system to break out of metastable configurations and hence become decorrelated from its initial configuration. After validating the equilibration protocol, which we refer to as random-walk molecular dynamics, the effects of the lipid composition and ceramide tail length on bilayer properties are studied. Systems containing pure CER NS, CER NS + CHOL, and CER NS + CHOL + FFA, with the CER NS fatty acid tail length varied within each CER NS-CHOL-FFA composition, are simulated. The bilayer thickness is found to depend on the structure of the center of the bilayer, which arises as a result of the tail-length asymmetry between the lipids studied. The hydrogen bonding between the lipid headgroups and with water is found to change with the overall lipid composition, but is mostly independent of the CER fatty acid tail length. Subtle differences in the lateral packing of the lipid tails are also found as a function of CER tail length. Overall, these results provide insight into the experimentally observed trend of altered barrier properties in skin systems where there are more CERs with shorter tails present.

Molecular Dynamics Analysis of Cardiolipin and Monolysocardiolipin on Bilayer Properties

The mitochondrial lipid cardiolipin (CL) contributes to the spatial protein organization and morphological character of the inner mitochondrial membrane. Monolysocardiolipin (MLCL), an intermediate species in the CL remodeling pathway, is enriched in the multisystem disease Barth syndrome. Despite the medical relevance of MLCL, a detailed molecular description that elucidates the structural and dynamic differences between CL and MLCL has not been conducted. To this end, we performed comparative atomistic molecular dynamics studies on bilayers consisting of pure CL or MLCL to elucidate similarities and differences in their molecular and bulk bilayer properties. We describe differential headgroup dynamics and hydrogen bonding patterns between the CL variants and show an increased cohesiveness of MLCL's solvent interfacial region, which may have implications for protein interactions. Finally, using the coarse-grained Martini model, we show that substitution of MLCL for CL in bilayers mimicking mitochondrial composition induces drastic differences in bilayer mechanical properties and curvature-dependent partitioning behavior. Together, the results of this work reveal differences between CL and MLCL at the molecular and mesoscopic levels that may underpin the pathomechanisms of defects in cardiolipin remodeling.

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.